- From: Eric Prud'hommeaux <eric@w3.org>
- Date: Thu, 21 Jun 2012 11:14:03 -0400
- To: public-semweb-lifesci@w3.org
I forgot to send these to the list last week. Apologies.
http://www.w3.org/2012/06/14-hcls-minutes
[1]W3C
- DRAFT -
SV_MEETING_TITLE
14 Jun 2012
See also: [2]IRC log
Attendees
Present
Regrets
Chair
SV_MEETING_CHAIR
Scribe
ericP
Contents
* [3]Topics
1. [4]Medicine Safety Code project
2. [5]simon_lin intro
* [6]Summary of Action Items
__________________________________________________________________
<matthias_samwald> argh
<scribe> scribenick: ericP
Medicine Safety Code project
matthias_samwald: presented a few months ago at AMIA
... BobF and simon_lin were there
... how do we give pharmacogenomic data to clinicians without too many
privacy or centralization issues?
<matthias_samwald> [7]http://safety-code.org/
matthias_samwald: also sidestepping the sluggish uptake of EHRs
... QR-code with the ~400 SNPs of most pharmacogenomic interest
... populated by microarrays or nextgen
... QR-code points a URL
... avoiding centralization
... genetic data is associated with many privacy issues:
... .. (personal) genetic data
... .. serves as a genetic fingerprint
<matthias_samwald>
[8]http://safety-code.org/v0.1/qm70W00I2KZ0u-A01N103HmXRp0W80080zIe0oWW
0vL4kC8441HTCCCfOA03U0uW020013mICe00I8wyFnk6Qo4m20e7Nq0m0500G03RG90e564
07xu6O0000000000000000000000000000
matthias_samwald: law in Austria avoids genetic data
simon_lin: this URL includes the data
matthias_samwald: exactly, ~250 chars. can be carried with you
BobF: so your URL will decode the data and present the info
matthias_samwald: yes
... you can interpret such a medicine safety code can be interpreted by
most phones
BobF: but your server is responsible for keeping the guidelines up to
date?
... that's not a trivial task
matthias_samwald: indeed. so far just a research datatype
<BobF> ericP - the questions were from BobF (not BobF) :-)
s/boyver/BobF/g
simon_lin: given your compression, how much info can you put in?
... i assume the size of the QRcode is a design constraint
matthias_samwald: putting lots of data in a code makes it very complex
and hard to scan
BobF: how many can you fit now?
matthias_samwald: i'm fitting ~400 SNPs. can't exceed ~800 with current
compression
ericP: this is good for 5 years?
matthias_samwald: around 10 probably
boycer: you've got a good set of phase I/phase II
... pharmacodynamics is what your body does
... there are a hand-full of enzymes for phase I (oxidizing/reducing)
... pharmacokinetics won't change much over the next years
<matthias_samwald>
[9]http://pharmaadme.org/joomla/index.php?option=com_content&task=view&
id=12&Itemid=27
boycer: but pharmacodynamics will explode over the next few years
... it's easier to predict pharmacokinetics
... but e.g. statin doesn't have a clear safe range
matthias_samwald: the 400 i use were compiled from the PharmGKB "VIP"
genes (those with existing clinical evidence)
... combined with a list from pharma adne (SP?)
... added also those listed in FDA drug labels
<boycer> Matthias - what was the pharma database (I heard Pharma ad &
e?)
<matthias_samwald>
[10]http://pharmaadme.org/joomla/index.php?option=com_content&task=view
&id=12&Itemid=27
<boycer> Found it: www.pharmaadme.org/
matthias_samwald: pharmacodynamics would seem more interesting than
pharmacokinetics, but the latter are further along
... CPIC SNPs are primarily kinetic
BobF: we're working on a schema for conveying guidelines which can be
hooked into a clinical support engine
... could you use that to update safety-code.org?
<matthias_samwald>
[11]https://docs.google.com/spreadsheet/pub?hl=en_US&hl=en_US&key=0AiGT
-vnkGcoLdFFVMEdqcFdYaDFqS0xHTnlUT0N3cEE&output=html
matthias_samwald: that'd be helpful
... in the last few days, i've updated this spreadsheet with CPIC and
Dutch Pharmacogenomics WG guidelines from PharmaGKB
... i'd like to further curate the data to create CDS rules in SPARQL
... but it would be great the have machine-readable CPIC guidelines
BobF: that's my goal
data:
application/medsafetycode+qrcode/qm70W00I2KZ0u-A01N103HmXRp0W80080zIe0o
WW0vL4kC8441HTCCCfOA03U0uW020013mICe00I8wyFnk6Qo4m20e7Nq0m0500G03RG90e5
6407xu6O0000000000000000000000000000
ericP: use RDF/XML with controlled schema? GRDDL? conneg?
matthias_samwald: i think RDF/XML is the worst of both worlds
... the rows in the spreadsheet represent multiple SNP combos
... we can break up some of the CPIC guidelines in this table into
smaller rows
BobF: i didn't intend to create a comprehensive pharmacogenomics domain
model
... just serialize CPIC guidelines
... there are national efforts in the US to create generic CDS rules
... i'd like to link the schema to those rules so there's a path from
the CPIC guidelines to what the hospitals can implement
ericP: how complex are these rules?
<matthias_samwald> example of guideline and boolean logic:
[12]http://pharmgkb.org/gene/PA128
BobF: most are single drug/geneotype combo
... warfarin is the most complex with a 2X2 matrix
<matthias_samwald> bite tge second row in the second table.
<matthias_samwald> note the second row in the second table
BobF: as we apply more systems bio, this will get more complex
... need to distinguish between broad clinical practics and specific
guidelines
... each institution will have to decide the latter
ericP: would you want your expressivity to cover quatitative dosing
even though you're not using all of that expressivity?
BobF: i'd like it to be extensible but i can't populate it now
matthias_samwald: the more complex the expressivity, the harder it is
for clinicians to understand and the harder it is to validate
boycer: is the safety-code.org infrastructure going to be public?
matthias_samwald: it's a jenna back-end and i'll make the SPARQL rules
open-source
simon_lin intro
UNKNOWN_SPEAKER: we're doing a trial looking at 80 genes via nextgen
... we're analyzing the impact of markers to see how we can change our
practice
... marshfield clinic also has an insurance subsidiary
... we'd like to put medicine safety codes and drug interactions into
an insurance card
... Mayo clinic and about 8 participants in Emerge
... expect recruitment next year
<boycer>
[13]https://www.mc.vanderbilt.edu/victr/dcc/projects/acc/index.php/Abou
t
[14]http://www.w3.org/People/Eric/ericP-foaf
Summary of Action Items
[End of minutes]
__________________________________________________________________
Minutes formatted by David Booth's [15]scribe.perl version 1.136
([16]CVS log)
$Date: 2012/06/14 16:08:59 $
__________________________________________________________________
Scribe.perl diagnostic output
[Delete this section before finalizing the minutes.]
This is scribe.perl Revision: 1.136 of Date: 2011/05/12 12:01:43
Check for newer version at [17]http://dev.w3.org/cvsweb/~checkout~/2002/scribe/
Guessing input format: RRSAgent_Text_Format (score 1.00)
FAILED: s/boyver/BobF/g
Succeeded: s/boycer/BobF/g
Succeeded: s/pharmacogenetics/pharmacokinetics/
Succeeded: s/put SNPs and drug interactions/put medicine safety codes and drug i
nteractions/
Found ScribeNick: ericP
Inferring Scribes: ericP
WARNING: No "Present: ... " found!
Possibly Present: BobF MacTed P15 Tony aaaa aabb boycer data egonw ericP https m
atthias_samwald scribenick simon_lin
You can indicate people for the Present list like this:
<dbooth> Present: dbooth jonathan mary
<dbooth> Present+ amy
WARNING: No meeting title found!
You should specify the meeting title like this:
<dbooth> Meeting: Weekly Baking Club Meeting
WARNING: No meeting chair found!
You should specify the meeting chair like this:
<dbooth> Chair: dbooth
Got date from IRC log name: 14 Jun 2012
Guessing minutes URL: [18]http://www.w3.org/2012/06/14-hcls-minutes.html
People with action items:
[End of [19]scribe.perl diagnostic output]
References
1. http://www.w3.org/
2. http://www.w3.org/2012/06/14-hcls-irc
3. http://www.w3.org/2012/06/14-hcls-minutes#agenda
4. http://www.w3.org/2012/06/14-hcls-minutes#item01
5. http://www.w3.org/2012/06/14-hcls-minutes#item02
6. http://www.w3.org/2012/06/14-hcls-minutes#ActionSummary
7. http://safety-code.org/
8. http://safety-code.org/v0.1/qm70W00I2KZ0u-A01N103HmXRp0W80080zIe0oWW0vL4kC8441HTCCCfOA03U0uW020013mICe00I8wyFnk6Qo4m20e7Nq0m0500G03RG90e56407xu6O0000000000000000000000000000
9. http://pharmaadme.org/joomla/index.php?option=com_content&task=view&id=12&Itemid=27
10. http://pharmaadme.org/joomla/index.php?option=com_content&task=view&id=12&Itemid=27
11. https://docs.google.com/spreadsheet/pub?hl=en_US&hl=en_US&key=0AiGT-vnkGcoLdFFVMEdqcFdYaDFqS0xHTnlUT0N3cEE&output=html
12. http://pharmgkb.org/gene/PA128
13. https://www.mc.vanderbilt.edu/victr/dcc/projects/acc/index.php/About
14. http://www.w3.org/People/Eric/ericP-foaf
15. http://dev.w3.org/cvsweb/~checkout~/2002/scribe/scribedoc.htm
16. http://dev.w3.org/cvsweb/2002/scribe/
17. http://dev.w3.org/cvsweb/~checkout~/2002/scribe/
18. http://www.w3.org/2012/06/14-hcls-minutes.html
19. http://dev.w3.org/cvsweb/~checkout~/2002/scribe/scribedoc.htm
--
-ericP
Received on Thursday, 21 June 2012 19:58:08 UTC